The SNP Consortium Ltd. said it completed a genome-wide SNP-based human linkage map - a map of the genetic markers called single nucleotide polymorphisms - and is making it available to researchers worldwide through its website.
"Linkage is where it's at, relative to beginning to find areas of the genome that are related either to disease susceptibility or to a response," Arthur Holden, chairman of the SNP Consortium, said. "To have a common linkage map to both disease studies and drug studies is very, very useful."
Holden noted that it is particularly significant that the map is publicly available, without companies having to pay licensing fees.
"The map provides a SNP-based resource for performing genome scans for disease genes," said Tara Matise, who directed the data analysis and construction of the linkage map at the Laboratory of Computational Genetics in the department of genetics at Rutgers University in New Brunswick, N.J.
"There are other linkage maps available that people have been using previously, but they take longer, they're less efficient and they also cost more," Matise said.
In terms of speed, the consortium said its map would allow genetic analysis to be completed in six weeks, compared to six to nine months required with less-dense microsatellite markers.
The consortium, based in Deerfield, Ill., said the linkage map includes "information about the relative location of one SNP to another, as determined by the likelihood that pairs or groups of SNPs move together from generation to generation."
SNPs are the most common genetic variation in human DNA. Formed in 1999 and supported by several pharmaceuticals firms, among other entities, the nonprofit organization has identified and mapped more than 1.4 million SNPs, making the information available publicly and free of charge.
"The consortium makes no money from this endeavor whatsoever," she said. "However, companies that are developing technologies for high-throughput genotyping can use this linkage set that we've developed to create platforms for SNP-based, high-throughput genome screening."
The map took about 18 months to develop, she said.
The SNP Consortium's members include the Wellcome Trust and a number of pharmaceutical and technology companies: AstraZeneca plc, of London; Aventis Pharma AG, of Frankfurt, Germany; Bayer AG, of Leverkusen, Germany; Bristol-Myers Squibb Co., of New York; F. Hoffmann-La Roche Ltd., of Basel, Switzerland; GlaxoSmithKline plc, of London; Novartis Pharmaceuticals Corp., of East Hanover, N.J.; Pfizer Inc., of New York; Searle (now part of Pharmacia Corp., of Peapack, N.J.); Motorola Inc.; IBM, of Armonk, N.Y.; and Amersham Biosciences, of Uppsala, Sweden.
Academic centers are the Whitehead Institute for Biomedical Research in Cambridge, Mass.; Washington University School of Medicine in St. Louis; Stanford Human Genome Center, of Stanford, Calif.; and Cold Spring Harbor Laboratory, of Cold Spring Harbor, N.Y., all of which are involved in SNP identification and analysis.
Orchid BioSciences Inc., of Princeton, N.J., performs third-party validation and quality control testing on SNPs identified through the consortium's research.